A synthesis of dryland restoration techniques.

Purpose

To quantitatively examine the efficacy of vegetation restoration in drylands globally.

Questions

  1. What is the global extent of research that directly examined restoration of drylands?
  2. What were the common measures?
  3. Is the restoration of vegetation a common and primary focus?
  4. How frequently does the restoration measure outcomes beyond the focal species?
  5. What were the primary restoration goals as reported by primary authors?
  6. How much variation was there in the techniques tested and how long were experiments monitored and tested?
  7. How relatively effective were the techniques?

Step 2. Sort

A summary of sort process using PRISMA.

library(PRISMAstatement)
prisma(found = 1504,
       found_other = 5,
       no_dupes = 1039, 
       screened = 1039, 
       screen_exclusions = 861, 
       full_text = 178,
       full_text_exclusions = 100, 
       qualitative = 100, 
       quantitative = 78,
       width = 800, height = 800)

Step 3. Synthesize

Check data and calculate necessary measures.

data <- read_csv("data/data.csv")
data <- data %>%
  mutate(lrr = log(mean.t/mean.c), rii = ((mean.t-mean.c)/(mean.t + mean.c)), var.es = ((sd.t^2/n.t*mean.t^2) + (sd.c^2/n.c*mean.c^2)))
data
## # A tibble: 3,291 x 48
##    study.ID    ID publication.year data.year exp.year `exp.length (mo…
##       <dbl> <dbl>            <dbl>     <dbl>    <dbl>            <dbl>
##  1        1   1.1             2018        NA       NA               NA
##  2        1   1.1             2018        NA       NA               NA
##  3        1   1.1             2018        NA       NA               NA
##  4        1   1.2             2018        NA       NA               NA
##  5        1   1.2             2018        NA       NA               NA
##  6        1   1.2             2018        NA       NA               NA
##  7        1   1.3             2018        NA       NA               NA
##  8        1   1.3             2018        NA       NA               NA
##  9        1   1.3             2018        NA       NA               NA
## 10        1   1.4             2018        NA       NA               NA
## # ... with 3,281 more rows, and 42 more variables: disturbance <chr>,
## #   focus <chr>, technique <chr>, paradigm <chr>, hypothesis <chr>,
## #   pathway <chr>, plant.species <chr>, target.plant <chr>,
## #   measure.success <chr>, measured.factor <chr>, factor.levels <chr>,
## #   treatment <chr>, control <chr>, unit <chr>, Nsites <dbl>, n.t <dbl>,
## #   n.c <dbl>, ntotalsamples <dbl>, mean.t <dbl>, mean.c <dbl>,
## #   sd.t <dbl>, sd.c <dbl>, se.t <dbl>, se.c <dbl>, `p-value` <dbl>,
## #   df <dbl>, measure.dispersion <chr>, lat <dbl>, long <dbl>,
## #   continent <chr>, country <chr>, ecosystem <chr>, `elevation
## #   (m)` <dbl>, `MAP (mm)` <dbl>, aridity.index <dbl>,
## #   `potential.evaporation (mm)` <dbl>, grazing <chr>, soil <chr>,
## #   notes <chr>, lrr <dbl>, rii <dbl>, var.es <dbl>
#consider adding some other effect size measures and/or study-level data too

Step 4. Summarize

Explore summary level data of all data. Explore aggregation levels that support the most reasonable data structure and minimize non-independence issues.

#evidence map####
require(maps)
world<-map_data("world")
map<-ggplot() + geom_polygon(data=world, fill="gray50", aes(x=long, y=lat, group=group))
map + geom_point(data=data, aes(x=long, y=lat)) #render a literal map, i.e. evidence map, of where we study the niche in deserts globally

#aggregation####
data.simple <- data %>%
  group_by(study.ID, paradigm, technique, measure.success) %>%
  summarise(n = n(), mean.lrr = mean(lrr), mean.rii = mean(rii), mean.var = mean(var.es))

se <- function(x){
  sd(x)/sqrt(length(x))
}

simple.data <- data %>% group_by(study.ID, paradigm) %>% summarise(mean.rii = mean(rii), error = se(rii))


#viz for aggregation####
ggplot(na.omit(data.simple), aes(technique, n, fill = paradigm)) + 
  geom_bar(stat = "identity") + 
  coord_flip() + 
  scale_fill_brewer(palette = "Paired")

ggplot(na.omit(data.simple), aes(measure.success, n, fill = paradigm)) + 
  geom_bar(stat = "identity") + 
  coord_flip() + 
  scale_fill_brewer(palette = "Paired")

Step 5. Statistics

Meta and conventional statistical models to explore relative efficacy.

library(plotrix) #for quick s.e. calculations sometimes needed for data tidy step
library(meta) #nice package for most meta-statistics

#assign model (typically a nice meta. function from one of several packages such as meta, metafor, or netmeta)
m <- metagen(mean.rii, error, studlab = study.ID, byvar = paradigm,data = simple.data) #fit generic meta-analysis to an object
m
##                         95%-CI %W(fixed) %W(random) paradigm
## 1    0.1004 [-0.0416;  0.2424]       0.5        3.9  passive
## 2        NA                          0.0        0.0  passive
## 3   -0.1868 [-0.2919; -0.0817]       1.0        4.2   active
## 4        NA                          0.0        0.0  passive
## 5        NA                          0.0        0.0   active
## 6    0.1973 [-0.1756;  0.5702]       0.1        2.0   active
## 9    0.1901 [ 0.1523;  0.2280]       7.5        4.6  passive
## 11       NA                          0.0        0.0   active
## 12       NA                          0.0        0.0   active
## 13  -0.0083 [-0.0913;  0.0747]       1.6        4.3   active
## 15       NA                          0.0        0.0  passive
## 16       NA                          0.0        0.0   active
## 19       NA                          0.0        0.0   active
## 20  -0.2808 [-0.3514; -0.2102]       2.2        4.4   active
## 21       NA                          0.0        0.0   active
## 23       NA                          0.0        0.0  passive
## 28       NA                          0.0        0.0  passive
## 29  -0.2971 [-0.3868; -0.2073]       1.3        4.3   active
## 30  -0.0326 [-0.1910;  0.1257]       0.4        3.7   active
## 31       NA                          0.0        0.0  passive
## 32       NA                          0.0        0.0   active
## 34       NA                          0.0        0.0  passive
## 35       NA                          0.0        0.0  passive
## 37       NA                          0.0        0.0  passive
## 39       NA                          0.0        0.0  passive
## 40       NA                          0.0        0.0   active
## 41       NA                          0.0        0.0  passive
## 42       NA                          0.0        0.0   active
## 43       NA                          0.0        0.0  passive
## 44       NA                          0.0        0.0   active
## 45       NA                          0.0        0.0   active
## 46       NA                          0.0        0.0  passive
## 48       NA                          0.0        0.0   active
## 50       NA                          0.0        0.0   active
## 51   0.1280 [-0.0646;  0.3205]       0.3        3.4   active
## 52       NA                          0.0        0.0   active
## 53       NA                          0.0        0.0   active
## 54       NA                          0.0        0.0   active
## 55       NA                          0.0        0.0   active
## 58       NA                          0.0        0.0  passive
## 59       NA                          0.0        0.0   active
## 61       NA                          0.0        0.0   active
## 63       NA                          0.0        0.0   active
## 64       NA                          0.0        0.0   active
## 65       NA                          0.0        0.0   active
## 66   0.0762 [ 0.0222;  0.1302]       3.7        4.5  passive
## 68  -0.1772 [-0.2845; -0.0699]       0.9        4.2   active
## 69   0.5020 [ 0.3552;  0.6489]       0.5        3.8  passive
## 71       NA                          0.0        0.0  passive
## 73       NA                          0.0        0.0  passive
## 74       NA                          0.0        0.0   active
## 76       NA                          0.0        0.0   active
## 77   0.0613 [-0.8629;  0.9854]       0.0        0.5   active
## 78       NA                          0.0        0.0  passive
## 80       NA                          0.0        0.0   active
## 82       NA                          0.0        0.0  passive
## 84       NA                          0.0        0.0   active
## 85       NA                          0.0        0.0   active
## 86       NA                          0.0        0.0   active
## 87  -0.0138 [-0.0406;  0.0131]      14.8        4.6   active
## 88  -0.1297 [-0.1597; -0.0997]      11.9        4.6   active
## 89       NA                          0.0        0.0   active
## 91       NA                          0.0        0.0  passive
## 93       NA                          0.0        0.0  passive
## 95  -0.2280 [-0.3094; -0.1466]       1.6        4.3   active
## 96       NA                          0.0        0.0  passive
## 98       NA                          0.0        0.0   active
## 100      NA                          0.0        0.0   active
## 101      NA                          0.0        0.0  passive
## 104  0.3069 [ 0.2619;  0.3519]       5.3        4.5   active
## 105      NA                          0.0        0.0  passive
## 106      NA                          0.0        0.0   active
## 107      NA                          0.0        0.0   active
## 108      NA                          0.0        0.0  passive
## 109  0.4675 [ 0.2613;  0.6737]       0.3        3.3   active
## 110      NA                          0.0        0.0  passive
## 111  0.0748 [ 0.0406;  0.1091]       9.2        4.6   active
## 112      NA                          0.0        0.0   active
## 114      NA                          0.0        0.0   active
## 115      NA                          0.0        0.0  passive
## 118      NA                          0.0        0.0   active
## 119      NA                          0.0        0.0   active
## 120      NA                          0.0        0.0  passive
## 121 -0.0229 [-0.0432; -0.0026]      26.0        4.6   active
## 126      NA                          0.0        0.0  passive
## 127      NA                          0.0        0.0   active
## 128      NA                          0.0        0.0  passive
## 129      NA                          0.0        0.0   active
## 130      NA                          0.0        0.0  passive
## 132      NA                          0.0        0.0   active
## 133      NA                          0.0        0.0  passive
## 134      NA                          0.0        0.0   active
## 135  0.0859 [ 0.0317;  0.1401]       3.7        4.5  passive
## 139      NA                          0.0        0.0   active
## 141      NA                          0.0        0.0  passive
## 142      NA                          0.0        0.0   active
## 143      NA                          0.0        0.0   active
## 145      NA                          0.0        0.0   active
## 146      NA                          0.0        0.0   active
## 147 -0.2642 [-0.4402; -0.0882]       0.3        3.6   active
## 148      NA                          0.0        0.0   active
## 149      NA                          0.0        0.0   active
## 151      NA                          0.0        0.0   active
## 152      NA                          0.0        0.0   active
## 153      NA                          0.0        0.0   active
## 154      NA                          0.0        0.0   active
## 155      NA                          0.0        0.0   active
## 157      NA                          0.0        0.0   active
## 160      NA                          0.0        0.0   active
## 161      NA                          0.0        0.0   active
## 162      NA                          0.0        0.0  passive
## 164      NA                          0.0        0.0   active
## 166      NA                          0.0        0.0   active
## 167      NA                          0.0        0.0   active
## 168      NA                          0.0        0.0   active
## 169      NA                          0.0        0.0   active
## 170      NA                          0.0        0.0  passive
## 171      NA                          0.0        0.0   active
## 179      NA                          0.0        0.0   active
## 180      NA                          0.0        0.0   active
## 182      NA                          0.0        0.0   active
## 188      NA                          0.0        0.0  passive
## 193      NA                          0.0        0.0   active
## 194      NA                          0.0        0.0   active
## 195      NA                          0.0        0.0   active
## 197      NA                          0.0        0.0   active
## 202      NA                          0.0        0.0   active
## 204      NA                          0.0        0.0   active
## 206      NA                          0.0        0.0   active
## 207      NA                          0.0        0.0  passive
## 209      NA                          0.0        0.0  passive
## 210 -0.3286 [-0.4648; -0.1924]       0.6        3.9   active
## 211      NA                          0.0        0.0   active
## 212      NA                          0.0        0.0   active
## 213      NA                          0.0        0.0   active
## 214      NA                          0.0        0.0   active
## 218      NA                          0.0        0.0   active
## 219      NA                          0.0        0.0  passive
## 220      NA                          0.0        0.0  passive
## 221      NA                          0.0        0.0  passive
## 223      NA                          0.0        0.0  passive
## 229      NA                          0.0        0.0  passive
## 230      NA                          0.0        0.0   active
## 231      NA                          0.0        0.0  passive
## 232      NA                          0.0        0.0   active
## 233      NA                          0.0        0.0   active
## 235      NA                          0.0        0.0   active
## 238      NA                          0.0        0.0   active
## 239  0.2968 [-0.1971;  0.7907]       0.0        1.4  passive
## 240      NA                          0.0        0.0   active
## 241      NA                          0.0        0.0   active
## 242      NA                          0.0        0.0   active
## 243      NA                          0.0        0.0   active
## 244      NA                          0.0        0.0   active
## 245      NA                          0.0        0.0   active
## 246      NA                          0.0        0.0   active
## 247 -0.3379 [-0.3809; -0.2950]       5.8        4.5  passive
## 248      NA                          0.0        0.0   active
## 250      NA                          0.0        0.0   active
## 251      NA                          0.0        0.0   active
## 252      NA                          0.0        0.0   active
## 253      NA                          0.0        0.0   active
## 254      NA                          0.0        0.0   active
## 255      NA                          0.0        0.0  passive
## 256  0.0430 [-0.0941;  0.1801]       0.6        3.9  passive
## 259      NA                          0.0        0.0  passive
## 262      NA                          0.0        0.0   active
## 263      NA                          0.0        0.0  passive
## 264      NA                          0.0        0.0   active
## 267      NA                          0.0        0.0  passive
## 268      NA                          0.0        0.0   active
## 269      NA                          0.0        0.0   active
## 271      NA                          0.0        0.0  passive
## 274      NA                          0.0        0.0   active
## 275      NA                          0.0        0.0   active
## 276      NA                          0.0        0.0   active
## 277      NA                          0.0        0.0   active
## 278      NA                          0.0        0.0   active
## 
## Number of studies combined: k = 26
## 
##                                          95%-CI     z p-value
## Fixed effect model   -0.0149 [-0.0253; -0.0045] -2.82  0.0048
## Random effects model -0.0109 [-0.0804;  0.0586] -0.31  0.7585
## 
## Quantifying heterogeneity:
## tau^2 = 0.0273; H = 5.92 [5.36; 6.54]; I^2 = 97.1% [96.5%; 97.7%]
## 
## Test of heterogeneity:
##       Q d.f.  p-value
##  876.35   25 < 0.0001
## 
## Results for subgroups (fixed effect model):
##                      k                     95%-CI      Q  tau^2   I^2
## paradigm = passive   8  0.0177 [-0.0043;  0.0396] 398.01 0.0642 98.2%
## paradigm = active   18 -0.0242 [-0.0360; -0.0125] 467.45 0.0200 96.4%
## 
## Test for subgroup differences (fixed effect model):
##                     Q d.f.  p-value
## Between groups  10.89    1   0.0010
## Within groups  865.46   24 < 0.0001
## 
## Results for subgroups (random effects model):
##                      k                    95%-CI      Q  tau^2   I^2
## paradigm = passive   8  0.1046 [-0.0800; 0.2892] 398.01 0.0642 98.2%
## paradigm = active   18 -0.0608 [-0.1339; 0.0124] 467.45 0.0200 96.4%
## 
## Test for subgroup differences (random effects model):
##                     Q d.f. p-value
## Between groups   2.67    1  0.1026
## 
## Details on meta-analytical method:
## - Inverse variance method
## - DerSimonian-Laird estimator for tau^2
#no difference in random effects model by paradigm but fixed yes. Hetereogeneity is significantly different so a. fixed not representative and b. need a better model
forest(m,  xlim="symmetric", plotwidth=unit(1, "cm"))